The San Jose Earthquakes were established in 1994 as San Jose Clash and competed in the inaugural Major League Soccer season in 1996. The franchise's name changed from the Clash to the Earthquakes in October 1999. Previously, a team from San Jose called The Earthquakes had competed in the North American Soccer League. The San Jose Earthquakes' main rivals are Los Angeles Galaxy and the two teams contest the California Clásico.

At the climax of the 2005 season, AEG, the club's owners, announced that the San Jose Earthquakes were moving to Houston, Texas as they were unable to find or build a suitable stadium in San Jose. After it was ruled that the San Jose Earthquakes name, records and legacy would not be transferred, the team's players and several coaches moved to Houston to form the MLS side Houston Dynamo. After two years of inactivity the Earthquakes returned in the 2008 season.

Since the turn of the 21st century, the San Jose Earthquakes have enjoyed significant MLS success. In 2001 they won the MLS Cup for the first time and a second success followed in 2003. The 2005 and 2012 seasons also saw the Earthquakes pick up the MLS Supporters' Shield and they finished top of the Western Conference in 2003, 2005 and 2012.

Over the years, San Jose have attracted several high-profile players to play for them, including Landon Donovan, Darren Huckerby and Dwayne De Rosario. Chris Wondolowski is the club's greatest goal scorer and Ramiro Corrales currently holds the record for most appearances.

The Earthquakes currently play their home matches at the Buck Shaw Stadium in Santa Clara, California. The ground, which has a capacity of 10,525, is shared with the Santa Clara Broncos. However, the team has plans to construct its own stadium in San Jose, California. Currently, it is hoped that the New Earthquakes Stadium will open at some stage in 2014.